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Switched mmtf -> bcif in examples; higher DPI for basic NMA plots #17

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Sep 27, 2024
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Switched mmtf -> bcif in examples; higher DPI for basic NMA plots #17

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8 changes: 4 additions & 4 deletions doc/examples/scripts/basic_nma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,15 @@
import biotite
import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.mmtf as mmtf
import biotite.structure.io.pdbx as pdbx
import matplotlib.pyplot as plt
import numpy as np
import springcraft

# Fetch G:T/U Mismatch-specific DNA glycosylase from E. coli
PDB_ID = "1MUG"
mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf"))
whole_structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True)
bcif_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))
whole_structure = pdbx.get_structure(bcif_file, model=1, include_bonds=True)
protein = whole_structure[struc.filter_amino_acids(whole_structure)]
ca = protein[(protein.atom_name == "CA") & (protein.element == "C")]

Expand All @@ -39,7 +39,7 @@
freq = eanm.frequencies()[6:106]

## Plot
fig = plt.figure(figsize=(8.0, 8.0), constrained_layout=True)
fig = plt.figure(figsize=(8.0, 8.0), constrained_layout=True, dpi=300)
grid = fig.add_gridspec(nrows=2, ncols=2)

ax00 = fig.add_subplot(grid[0, 0])
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6 changes: 3 additions & 3 deletions doc/examples/scripts/normal_mode.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
import ammolite
import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.mmtf as mmtf
import biotite.structure.io.pdbx as pdbx
import numpy as np
import springcraft

Expand All @@ -31,8 +31,8 @@


# Load structure
mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf"))
structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True)
bcif_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))
structure = pdbx.get_structure(bcif_file, model=1, include_bonds=True)

# Filter first peptide chain
protein_chain = structure[
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